Neon Genesis Evangelion the Uzumaki Chronicles
by Shinji Auditore Ikari
Summary: Shinji is abandoned by his father agter his mother disappears. He goes to the shadow demension. I don't own Evangelino or Naruto
1. Chapter 1

Chapter 1:Shinji 'Oni of the Shadows' Uzumaki

Today was the day Shinji had to return to his dimension. The day he never wanted to come to pass. The day he had to return to Tokyo 3 and the day he had to face his father.

**Flashback**

Shinji Ikari, a four year old boy, ran through the streets of Tokyo 2. His mother had mysteriously disappeared earlier that day and his father had abandoned him moments later. If he thought things couldn't get any worse he was wrong. After he started to run a liquid landed on his left eye and had blinded it. He ran down an alley and noticed he was in a cave with a door at the end of it. Curious he started walking towards the door. He saw the door was ajar and opened it slowly.

"Hello" he asked slightly on edge.

Hearing no reply Shinji walked into the room. Looking around he saw weapons around the room, but the strangest thing of all was the picture on the roof of the room. The picture looked like a fox demon with a ball of energy in its hand and across it was a bat demon with lightning around its hand, but the really strange thing was that the picture was moving and it looked like the demons were fighting each other.

"What is that "Shinji thought out loud?

"**It is the final battle between Naruto Uzumaki and Sasuke Uchiha that had dictated the fate of the village of Konoha"A voice said.**

"Wh- who are you?"Shinji asked clearly frightened

"**I am the Guardian of the Gateway, there is no need to be afraid Shinji Ikari" **The guardian said

"I'm sorry if I'm trespassing, I didn't mean to."Shinji exclaimed" Sorry"

"**It is ok Shinji; there is no need to be sorry."** The Guardian told Shinji**" You Shinji Ikari have a great destiny to fulfill; I can take you to the shadow dimension where you can prepare for it or you can stay here and wait. You will fulfill your destiny no matter the choice but what happens after you have fulfilled will change depending on the choice you make."**

"But where would I prepare for my destiny?"Shinji asked the Guardian

"**The gateway I protect is a portal to the shadow dimension. A place different from this one. But the question still stands will you go to the shadow dimension or will you stay here."** The Guardian replied

"I want to go to the Shadow dimension, I want a new life. I have nothing left in this world anymore."Shinji said confidently

"**Don't think you don't have anything left Shinji Ikari, now go and make yourself a new life. Good luck."** The guardian told him

And with that Shinji for the first time noticed a door on the other side of the room. Walking towards it he saw there was a piece of paper with the Japanese Kanji for seal. A few second later it started to burn and the door opened revealing a red portal with green flames on the edges.

Before Shinji stepped through the portal he told the Guardian, "Thank you for giving me a chance at a new and better life" and with that he stepped through the portal.

What he felt was very different from what Shinji expected, it felt like his was being thrown around and that his own body was attacking itself. After a full minute of this it suddenly stopped and Shinji was thankful just before he fell into unconsciousness.

Fortunately for Shinji squads of Anbu Black Ops were patrolling around the village of Konoha. When they saw the boy all of them ran to assist the poor boy.

"What happened to him" one of them asked.

"That doesn't matter right now, you" another said pointing to one in front of him," Get him to the hospital and you come with me. We need to alert the Hokage. He finished and they stared running.

**In the hospital**

"Hinata, Sakura. This boy needs help." The Anbu Black Ops member told them

"Oh my gosh, what happened to him?" Hinata asked him

"We don't know, we found him outside the village like this."The man said" Can you help him?"

"Yes, get him on the bed now."Sakura told the man.

"Yes, ma'am."

**Hokage's Building**

'I really hate paperwork' Naruto thought to himself.

He then heard a knock on the door and saw two Anbu Blacks Ops members.

"What's happened?" Naruto asked them.

"Lord Hokage, we found an injured boy just outside the village and we sent another member to take him to the hospital." One of them told him.

"How badly injured was he?" Naruto asked them.

"He had multiple wounds, none of them too severe." The other told him.

"Ok return to your patrol and report back to me later." Naruto told them standing up.

"Yes, sir." They said in unison.

**In the Hospital**

Naruto burst through the door shocking Hinata and Sakura," Where is he." Naruto asked them out of breath.

"He's on the bed. But he's still unconscious." Hinata told him.

Sakura and Hinata started telling Naruto about his wounds and how they could have happened." Who would do this to a four year old boy" Sakura asked sadly.

"I don't know but we'll make them pay Sakura."Naruto told her.

After a few more minutes of talking, Shinji started to stir. Naruto was the first to see this and he got to his feet and made his way to the side of the bed.

When Shinji woke up his body felt really sore. When he opened his eyes he was surprised by three strangers standing by the bed he was in.

Startled Shinji curled up in to a ball and chocked out," Who are you."

Knowing that the boy was scared Hinata walked up to him slowly and introduced them," Hi I'm Hinata Uzumaki, that is my husband Naruto," she said pointing to him," and that is Sakura Lee. What's your name?" she asked him.

"I'm Shinji." The boy said.

"What happened to you Shinji, how did you get hurt?"Hinata asked.

He then told them what happened to him that day his father abandoning him, getting blinded in his left eye and how he met the Guardian.

"Sakura, can you please go get Ino."Naruto asked her.

"Yes Naruto, but why do we need her?" she asked.

"We need to see if he's telling the truth."Naruto explained to her.

When she left they started talking again and a couple minutes later Sakura returned with Ino trailing behind her.

"Yes Naruto?" she asked him.

"Ino, Shinji here told us a very interesting story and we need you to see if he was telling the truth."Naruto told her.

"Sure thing" she replied."Hey Shinji, I'm just going to look if the story you told us was true." she explained to him

"Yes, Ma'am" Shinji answered politely.

After he answered her she made a series of hand signs and said," Mind Transfer Jutsu."

When she was done she stood up and told Naruto," He's telling the truth Naruto."

"Well then it looks like he's got nowhere to stay." Naruto thought out loud.

When he said that Shinji thought where he is going to live and eat, how can he fulfill his destiny if he dies. When he thought that he was on the brink of tears. Naruto saw this and moved closer and put a hand on his shoulder and told him," Hey Shinji, you can stay with us if you to."

"Really," Shinji asked looking up hopefully," I don't want to be a burden."

"It's not a problem at all Shinji. If you want we can adopt you into our family."Hinata told him reassuringly.

"I can have a family." Shinji said smiling

"Yes Shinji, you can have a family." Hinata and Naruto told him pulling him into a hug.

"Welcome to the family, Shinji Uzumaki." Naruto said with a smile on his face.


	2. Chapter 2

Chapter 2: The arrival of …. Shinji?

Shinji Uzumaki was walking through the streets of Tokyo 3 wondering where this so called transport of his was. Yesterday the Guardian had contacted him telling him that it was time to leave the Shadow Dimension and return to his own. When he returned he noticed he was fourteen again.

**Shinji was having a great day. A very successful mission completed, having fun with his friends for the rest of the day and to top it all off today was June 12th. It was his 27****th**** birthday. He knew his friends were going to throw a big party for him. Right then the Guardian had to contact him of all times.**

"**Shinji, it is time."The Guardian told him.**

"**How long do I have to say goodbye?" Shinji asked in an almost pleading voice.**

"**You can have a week to say goodbye to your friends and family. Unfortunately I cannot give you any longer." The Guardian told the boy **

**With that Shinji ran off to give his parents the bad news. First he had to find his mom and ask her to meet him in his dad's office. Hinata agreed but was curious as what it was that he was going to tell them. 'Please don't let it be that time.' She knew very well that Shinji had to someday return to his own dimension and face whatever danger lays in wait for him. While Shinji was looking for his closest friends to tell them all together Hinata and Naruto where talking about what it could be that he needs to tell them so urgently.**

"**Do you think that it is time that he needs to return to his own dimension?" Hinata asked with worry in her voice.**

"**I think it may be that he does needs to return."Naruto told her," but don't worry he'll come back after he's taken care of the trouble in his dimension." He added reassuringly.**

"**Yea, your right. I'm just going to miss my son a lot."Hinata replied.**

"**Hinata you worry too much. He'll be fine."Naruto told her.**

**Just then another five people walked into Naruto's office and they saw that it was Shinji's friends so they assumed he wanted to tell them all together. After about five minutes everyone found a seat and quieted down when Shinji walked in.**

"**Hey everyone I called you all here today because I have very important to tell you."Shinji told all of them" as you all know I came from another dimension to this one with the help of the Guardian of the Gateway. Well a while ago he contacted me and told me I had to leave in a week's time. I know this is all really bad timing but I have to face my destiny there and soon. You don't have to worry about me because I will come back and anyone who challenges me is stupid crazy or both."Shinji told them. **

**The last comment got a chuckle from the group.**

**When he finished talking Hinata and Naruto walked up to him. Naruto decided to make a joke, so when he reached Shinji he told him," Remember Shinji, when you return bring back a girl" he said giving a foxy grin which got him a smack on the back of his head.**

**Hinata decided it was her turn to speak," Besides what your father just said, I'm going to miss you a lot Shinji." She said pulling him and his father into a hug.**

"**I'm going to miss you too mom, dad." He told them returning the hug. **

**When they finished Shinji turned to his friends." Don't worry I'll be back to beat you guys in sparring" he said jokingly. **

**Tomorrow his dad called him to his office to give him something as a going away gift. When he got there his dad was pacing through the room like he was going insane.**

"**Hey dads, what's wrong you look like you're going crazy?"Shinji asked when he walked in.**

"**Oh hey Shinji, I want to give you very special going away gift."**

"**Sure dad, what is it."**

"**Shinji I want to give you my Sharingan eye."Naruto told him.**

"**What no dad I couldn't." Shinji told him.**

"**Shinji, you should go back to your dimension with both your eyes working. Not with you being blind in one of your eyes."Naruto explained to his son.**

"**Ok, if that's really what you to give me dad."Shinji said still a little unsure of receiving his father's eye.**

"**The operation will take place at midday tomorrow."Naruto told Shinji" and one more thing Shinji whatever you do in your dimension. Know that will always be proud of you my son."**

"**Thanks dad" Shinji replied with a smile on his face.**

**The next day the operation went smoothly and as planned.**

**While Shinji was packing his things he found his old SDAT player. He hadn't seen it in over Ten years. He decided to listen to Beethoven's Ode to joy and before he knew it, it was time to go back to his dimension.**

Shinji visibly flinched as he did not want to remember the actual goodbye with his parents and his friends. A shockwave brought him out of his thought and as he looked up he saw a giant black humanoid figure walking and being shot at with missiles. Shinji watched and wondered how the beast could get hit by all those missiles and not have a scratch on itself.

Shinji was about to bite his thumb and perform a summoning Jutsu when he heard tires screeching and when he turned to his right he saw a blue Renault speeding towards him. Shinji was about to jump over the car when it turned and the door opened.

"Get in" the driver yelled.

Shinji wasted no time in climbing into the passenger's side of the car. She got the car away from there and the angel's foot hit the ground where the car was a second ago.' One thing I can say about her is that she knows how to make an entrance" Shinji thought to himself.

"Hey sorry I'm late, names Misato Katsuragi."Misato told him.

"Sorry enough to have been here fifteen minutes earlier?" Shinji joked.

"Ha Ha very funny Shinji Ikari," she said

Shinji visibly flinched when she said Ikari. Misato noticed this.

"Hey, what's up? "She asked him concerned.

"Uzumaki."Shinji told her.

"What." She questioned curiously.

"My name is Shinji Uzumaki. The name of my true Father, Naruto Uzumaki."

"I thought your father was Gendo Ikari" Misato asked him confused.

"I had forsaken him ten years ago"Shinji told Misato seriously

" I guess you really hate Gendo then hey," Misato said thinking he would be comfortable not calling Gendo his father.

"Yep, what about you and your dad."Shinji asked curiously

"We are very much the same Shinji ik- Uzumaki."Misato said almost slipping up

"That doesn't answer my question" Shinnji told her almost threatingly.

"I hate my father," Misato said sorrowfully.

"Hey Misato it's ok, everybody has a loss sometime in their lives."Shinji said quickly adding," We are here."

"Oh yeah, did Gendo send you an I.D. card."Misato asked

"Nope," He told her straight.

Just then the GeoFront came into view."Can I swim in there" Shinji asked pointing to the lake.

"Uhh- I don't know really." Misato answered awkwardly.

"We're lost aren't we," Shinji asked for the tenth time.

"No, we're just taking the scenic route." Misato told him.

'Why does this map have to be so complecated' she thought sadly.

"Yo Misato let's take the elavator." Shinji yelled

"Sure" only now did Misato notice what he was wearing- a black turtle neck with a jacket vest that had loads of pockets filled with scrolls, camo pants and boots.

When they got to the second floor Shinji was reading his Manga Ranma 1/2 and when the elavator doors opened a blonde doctor wearing a blue bathing suit and a lab coat walked in.

"H- hi Rit- suko" Misato managed to stutter.

"Why are you wasting my time Captain. Don't you know we're short on time and man-power." Ritsuko demanded.

"Damn you sound like Grandma Tsunade."Shinji told them.

Ritsuko pretended not hear that and said," so he's the third child."

"Yes I am and you would be wise not to anger me," he told her threatingly.

Ritsuko was appaled that someone talked to her like that let alone a child.

Ritsuko led them to a doorway and Shinji put away his Manga noticing it was dark inside.

"Turn on the lights please" Shinji asked no one in particular.

When the light turned on Shinji saw a giant bio-mechanical head.

"This is mankinds salvation. The bio-mechanical fighter know as Evangelion Unit 01." Ritsuko announced.

"I have one question." He told her.

"And what's that's," she asked curiously.

Whoever did the paint job sucks, can you change it?"He told her.

"You can discuss that later." A voice rang out.

Looking up Shinji saw the source"Hello Gendo". Shinji said coldly.

" You will pilot Eva Shinji." Gendo said.

" And if I don't your going to use the girl on the other side of the door." he said ," I will pilot it if you bring her in here or else."

"Or else what." Gendo said mockingly.

In a flash Shinji grabbed a kunai and threw it at Gendo breaking through the glass and breaking his glasses. The point an millimeter from his face.

"Or the next one goes through your head."Shinji threatened.

"V- v- very w- ell" Gendo croaked

A second later a nurse pushed in a girl on a gurney that had blue hair, red eyes and several bandges.

" Stand back" Shinji warned. He then proceded to do several hand signs and said" Medical Jutsu: Angel's Cleansing light."

Rei's body glowed light blue for several seconds before fading. What they saw shocked them, Rei was standing in front of Shinji looking into his eyes.

The building then shook and a few beams fell down from the roof. Shinji prepared to perform a second Jutsu when he felt a huge chakra surge in the room and the Eva's hand moved to protect him and Rei.

"The Eva activated itself." A women yelled.

"That's not possible, the plug wasn't even inserted." Ritsuko exclaimed.

" I'll pilot now." Shinji told them, giving Rei a quick peck on the cheek and then proceeded to walk towards Misato.

Rei was shocked to raised her hand to her cheek and for the first time smiled.


	3. Chapter 3

Chapter 3: Shinji Uzumaki, the unknown.

While they were getting Shinji and his Eva prepped for battle with the angel, Rei thought why Shinji had threatened commanders Ikari's life to bring her into the Eva holding Bay. Rei then thought to when he kissed her. Did he like her? She then stopped herself, why was she thinking of such trivial things.

She was interrupted from her thoughts when she heard Major Katsuragi yell" EVA launch."

Shinji yelled over the com," yahoooooooooo." 'they should turn this into a rollercoaster ride' he thought to himself. When the eva stopped he saw the angel a kilometer away from him.

"Ritsuko, what are these clips on my head." Shinji asked the scientist.

"They are A-10 neural clips, they help you connect with your Eva." She told him

"Wow his synch ratio is at 44.3 with no prior training or knowledge of Eva." Ritsuko thought out loud

"Misato retract the launch pad, it's going to get in my way,"Shinji said over the com.

Misato was confused," Shinji, are you sure?" she asked him.

"Yes." Shinji then started to use the neural clips as a medium and spread his chakra throughout the Eva.

"uhh ma'am you should come look at this," Maya told Ritsuko.

"WHAT, his synch ratio is 99, 6."Ritsuko exclaimed very confused.' That's so close to the berserker state.' Ritsuko thought to herself.

Shinji then ran towards the angel grabbed it by the waistand threw outside the city,'this sholud be good enough, no one can get hurt out here'Shinji thought ot himself.

Shinji putting up the Eva's hand and showed the angel the universal ' bring it on' gesture. The angel slightly confused just stood there waitingfor the Eva to do something. Unit 01 raised its hand again pulling the middle finger at the angel and gestured 'bring it on' again and then settling back into a fighting stance. The angel getting the message this time charged at Unit 01 extending its energy lance from its arm. Shinji dodged the stab and snapped the lance in half throwing it back at the angel. The angel shrieking didnt see Eva Unit 01 perform a series of hand signs,"secret jutsu, Thousand years of Death,"he finished jumping behind the angel and crouching, it then pointed its forefingers together and...

"Did he just...?"Misato asked back in the command center

"Yes, he stuck the Eva's fingers up the angels ass,"Ritsuko.

"Shinji, stop fooling around and get serious."Misato yelled at him.

"Ok ok jeez. Hells Binding Chains Jutsu." he performed the Jutsu and stuck the Eva's hands in the ground.

Seconds later gold chains with a black aura burst from the ground and tied themselves around the angel and holding it securely in place. When the angel's eyes flashed white to shoot him he didn't try to move the Eva. A second later the light died down. Shinji knew that not only did the chains hold the target in place but also drained them of the chakra they tried to gather or use. "next time don't mess with Shinji' Oni of the Shadows' Uzumaki. Shinji then held out the Eva's hand and a blue ball of energy started to gather in it." Rasengan" Shinji yelled out and hit the angel's red core with it. When the core cracked the unstable power within the core exploded and engulfed unit 01.

"Noooo, Shinji."Misato yelled.

"Stop yelling Misato. I'm fine."Shinji said over the com.

"Shinji, you're ok? "Misato asked in disbelief.

"Yes Misato, I'm ok. Now can you open the launch pad so I can come back?"Shinji asked her.

"Ye- Yea sure Shinji." Misato stuttered

Back in the launch bay" Hey Misato, how did I do?" he asked before he fainted.

**Three hours later.**

Shinji was slowly waking up when Rei sat down next him. The first thing he noticed that he was on a hospital bed and that Rei was sitting next to him."Hey Rei, what are you doing here? Did Gendo tell you check on me?" He asked her.

"No, I came here on my on my own accord. Why did you refer to yourself as Shinji 'Oni of the Shadows' Uzumaki?" Rei asked

"Uzumaki is the last name of my true father and my friends call me 'Oni of the Shadows' because I attacked my enemies from the Shadows without warning." Shinji told her," Hey Rei."

"Yes Shinji."Rei answered him.

"Do you want to go on a date with me on Friday?"Shinji asked her.

"I will ask the commander and if he says yes I shall go with you."Rei told him.

"Rei, if you ask him then he will forbid you from going with me."Shinji explained to her.

"Very well, if he does not ask I will not tell him."She told him after a moment of consideration.

"Shinji why did you faint after you stepped out of the Eva?" She asked him.

"I fainted because I exhausted too much of my chakra in the Eva."Shinji told her.

"What is chakra?"She asked curiously.

Shinji then went on to explain to Rei what Chakra is and the basics. "Chakra is made up of to woo different types of energy, Physical and Spiritual energy. Physical energy is made up of your Stamina and your Spiritual energy is made up from your past experiences."

"Shinji, can you please teach me to be a Shinobi?"Rei asked him hopefully.

"Yea, I'll teach you how to become a Shinobi, but you cannot tell Gendo or he will stop you for learning."Shinji told her

"Understood Shinji." Rei replied

"You're doing what." Ritsuko yelled at Misato over the phone.

"You heard me, I'm taking Shinji to live with me."She said looking at Shinji who was reading manga." It's already been approved and everything. And don't worry I won't be making any passes at him."

"OF COURSE YOUI WON'T WHO WOULD EEVN CON-."Ritsuko continued yelling.

"Some people can't take a joke." She told Shinji.

"Welcome Home, looks like they already delivered your stuff. I just moved I here myself, so it might be a little messy." Misato told Shinji.

When the door opened Shinji was shocked. There were dozens of beer cans lying around on the tables and floor. Trash lying everywhere and bra's and panties all around the room. Shinji thought to himself,' She calls this a little messy, and this is just the first room.

"Welcome home Shinji." Misato told Shinji smiling.


	4. Chapter 4

Chapter 4: The oni going to school

The first night Shinji moved into Misato' apartment it was messier than a pigsty. Shinji decided after he ate Misato's sorry excuse for dinner that he would take a bath anc then afterwwrds clean the house.

Shinji got out of his clothes and wlked towards the bathroom and when he opened the door hefelt something brush against his legs. Looking down he saw a penguin guessing it was the pet that misato mentioned during dinner.

Shinji bent down and scratched the penguin on the head." He little guy, i'm Dhinji Uzumaki. Your new room mate." he told the penguin shaking its fin.

The only reply Shinji got from the animal was,"Wark."

Later that night when Shinji was lying on top of his bed. He heard his door open and turned his head to see Misato." Shinji are you awake?"Misato asked him.

" Yes Misato."Shinji answered her.

"Shnji, i want to tell you that you did a very great thing today. You saved this city."Misato continued.

"I didn't kill the angel to save the city, i did it to protect those precious to me. I did it to protect you and another Misato," Shinji told her.

"Wow, thanks Shinji." she said walking over to him and giving him a hug.

"No problem Misato." Shinji said returning the hug"Goodnight."

The next two weeks Shinji began his training in Eva and his date with Rei the previous Friday went wonderfully. " I wonder why he agreed to pilot Eva again?"Ristsuko asekd Misato.

"He told me it was to protect those precious to him."Misato told her.

"How's he doing at school."Ritsuko asked her.

"Great,every morning he goes to school with some of his friend, he really popular. He gets lots of phonecalls on the cell phone i gave him a while back and you wouldn't believe how many messages there are on my answering mmachine when he won't pick up the phone."Misato told her.

"Sounds like he' having a great time."Ritsuko said smiling.

Just then Shinji's voice chimed in."Hey Ritsuko."

"Yes Shinji"she answered him.

"I really don' think the rifle could be that effective in battle, so can you make me kunai's and could you also change the colours of the Eva."Shinji asked.

"Sure Shinji what colours do you want."She asked with some venom in her voice because she chose the colour scheme.

"How about gun metal gray with neon blue trimming." Shinji answered her.

"Sure Shinji, i'll pass that to the R&D labs later."she told him"Ok Shinji, you can get out now, trainings finished.".

Shinji and Rei's date

While Shinji waswalking towards Rei's apartment he thought about what they were going to do was going to take her to the mall for a snack, then seeing as she didn't really know how to have fun he would teach her and then to top it all of a walk around the park. When Shinji got to her apartment he pressed the buzzer. After ten seconds nothing happened so he knocked on the door. Two seconds later the door opened and Shinji saw Rei. She looked great but the only problem was that she was that she was wearing her school uniform. He dcided not to say anything about it now.

"Helllo Rei, are you ready?"He asked her.

" Yes Shiinji I am ready to leave."Sh e tolddhim in a onotone voice..

"Great let's go then."Hesaid happily.

When they got to the mall Shinji took her to eat at a restraunt. Rei was quiet for a few minutes so Shinji decided it was up to him to start the conversation.

"SO Rei, what do you do when you're not in school or at Nerv."Shinji asked her.

Ï go home eat and wait for the next day to start."Rei replied

Shinji was shocked that anyone couuld live like that," Is tht relly all you do Rei."Shnji asked her.

" Yes, it iis sufficient for my needs." Rei told him with no emotion.

" And is your school uniform the only clothes that you own?" Shinji asked hoping she would tell him no. He was wrong.

" Yes, I do not need any thing else."Rei said.

When they were finished eating Shinji took her to a bench and talked to her."Rei, who told you that you only have to do what you need to and only have on pair of clothes?"Shinji asked her.

"The commander did."Rei anwred him.

"Wow, this is gonna be harder than i thought. Rei you can do anthing you want to when your not on duty or at school. You can make your own choices and dictate your own actions. You can have fun whenever you want. Come on Rei I'm gonna show you how to have fun." Shinji told her sttanding up.

First they went to the arcade ad played games for half an hour. They played game like dance dance revolution, street fighter and when they finished Rei actually smiled at Shinji when they left. It was small but Shinji returned her smile with one of his.

" Ok Rei, now here."He said giving her ¥40000." Now I'll give you half an hour to go and get yourself new you come back I want you to have at least six new outfits."

" Yes Shinji." She said.

When she left Shinji took out his Manga and read from where he stopped last time he read. By the time Rei got back Shinji had fallen asleep with his Manga on his face and she had eleven new lighty tapped Shinji on his shoulder and stirred slightly but he didn't wake up. She needed to try something else. She decided to push him off the bench to see if he would then wake up. When she started pushing him lightly Shinji felt that he was being pushed lightly. He knew if he let them push him any further he would fall of the bench.

"You know you could have just shook me or yelled at me to wakke up, right Rei?" He asked he scaring her slightly.

" I tried t wake you up but you wouldn't and i didn't know what else to do ." she explained to him..

" Ok nevermind, let's see what you got for yoursellf. Wow this is really nice. Shinji saaid when he pulled outt a light blue sundress.

" Yes, i liked this one the best as well. I also bought two outfits for our training." She explained to him.

" Nice work Rei." he told her giving a small hug."come on let me take you home." Shinji continued standing up.

The walk back to her apartment was quiet since neither knew what too talk about. When they got there Shinji decided to speak but Rei beat hiim to it.

"Thank you Shinji for a wonderful time tonight." she thanked him

" Your welcme Rei, i hope we can do this sometime agaain. Shinji said." Goodnight Rei" at which point he gave her a hug for which he was glad she ereturned

"Goodnight Shinji" she said a gave him a quick peck on the lips and quickly slipped into her apartment.

Shinji was lost in thought while he walked home,' I know she likes me but i didn't think ahe would be this forward.

When he got hom he noticed Misato was stilll awake and she decided to tease him te second he walked htrough the door.

"Hey Shinji, so tell me. Is Rei a good kisser?" Misato asked him in a teasing voice.

Then Shinji did the thing that Misato hates so much," Excuse me Misato, did you say something?" he aasked inoccently.

A vein nearly popped out of her forehead."Good night Misato." Shinji said to her going to his room. That night Shinji slept with smile on his face.

The next morning

Shinji wwoke up this morning feeling better than ever. When he had eaten breakfast and gotten into his school uniform ad he yelled standingin front of Misato's room."Hey Misato. Wake up, its morning."

" Ug, Shinji 've been working night duty and i just got back aa few minutes ago so pllease just let me sleep." She told him.

" Ok but your wasting perfectly good morning." He told her walking out the door and going to school.

When Shinjni got to school he saaw that Rei was in her usual seat looking out the window. After Shinji walked into the class the class rep waled in and was looking for specific stuent. The student in question was Kenske and he was sitting at tthe back of the class playing with aa model airplane since he wa a military otaku.

" Mr Aida" she said in a menacing tone walkig to his desk." Did you give mr suzaharra the bullitens."

" I rang the doorbell but nobody was home so..." He told her.

" Mr. Aida i thought you were Toji's friend. Don't you care about him?" She exclaimed asking him.

He was about to reply the classroom door opened and Toji walked in wearing his usual tracksuit.

"Where is everyone? Did they disappear or something?"Toji asked.

Kenske tells hm," Most people left the city because of the last battle. So where were you yesterday."He added.

"I visited my sisterin the hospital. Shewas in a car crash last month and my family can't afford for the opperation to fix he legs. Why did that idiot have to drive so fast and crash into her car."He said yelling the last part.

AFer class Shinji was caught up by Toji outside on the field.

"HEY, new kid."Toji yelled at Shinji

Shinji turned to see Kenske and Toi walking up to him.

" I'm gonna give you a welcoming present"He told Shinji." Its an initiation i give to all new students."

" Ok fine, but i won't take it lying down." He replied.

Toji threw the first punch which Shinji caught and the next punch he threw Shinji also caught. Toji tried to throw a ick at Shinji but before it could connect Shini threw Toji into a backflip. ' what the hell just happened'Toji thought to himself. He got up a second later and he saw that Shinji was nowhere too be seen but then suddenly his voice echoed from all around them." Sand style: Headhunter Jutsu." After Shinji said that his feet fell through the ground and he only stopped with his head above the ground.

"Had enouggh Shinji" asked him apppearing in front of him in a puff of white smoke.

" Yes, Shinji-sensei. Please teach me your ways." Toji yelled while Shinji pulled him out of the ground.

Kenske joned oji andthey both bowed to Shinji and chanted" Please Shinji-sensei, teach us to fight." Shinji considred this he thought that he was already going to train Rei he might as well start a team." Ok i'll teach you but go to a shelter 's go Rei." he said and a second later they botth disappeard in a puff of smoke and at the same time the angel alarm went off. With that Toji and Kesnke ran to find a shelter.


	5. Chapter 5

Chapter 5: Disobe+ying orders and team Oni.

As they got to Nerv Shinji dropped Rei off at the command center and went to the changing room and then proceeded to get into his Eva's entry plug." What's the angels status." Misato asked maya, Shigeru and Makoto.

"It's been intercepted by the army artillery defense but has no wounds or signs of damage. It's almost mad it into the city." Shigeru replied to the major.

Meanwhile Ritsuko was explaining to Shinji where the Eva's new weapons were and how to access them. "The kunai's are on top of the left, while your shurikens are inside the Eva's shoulder." She told him

"Eva Launch." Misato yelled and with that the Eva sped towards the surface.

The Eva appeared in one of the buildings and got out of it. Opposite it was another building in which was a rifle. Shinji took the rifle and turned to face the angel. It looked more like a bug than anything else. When Shinji turned his Eva the angels body straightened up and purple glowing tentacles appeared out of nowhere on either the of the angel. Shinji decided to do an unorthodox and aimed the rifle at the ground at the Eva's feet and fired throwing up large amounts of dust. When Shinji was sure that the angel couldn't see him he stealthy made his way around the smoke screen he created until he was on the other side of the angel. Meanwhile the angel was blindly slashing its whips through the smoke hitting nothing but air. Shinji reached up to the Eva's right shoulder and grabbed two shurikens and a kunai from the Eva's left wrist. After neutralizing the Angels A.T. Field, he jumped up over his cover and the shurikens at the angel which lodged in its back. Screeching the angel turned around and faced a Unit 01 and its Shinobi pilot.

Just then Misato spoke to Shinji over the com." Shinji there are two civilians on the mountain side. Abort the mission grabbed them and retreat to extraction point A-43."

" No if i don't kill the angel now it will kill us." he told her noticing that the age had cut his Eva umbilical cord and that he had only 2 minutes of internal battery power left.

Shinji ran full speed towards the angel with his Kunai ready to strike. "Sharingan." Shinji yelled knowing he would need it to dodge the angel's attacks. As the people on the command bridge watched they saw Shinji get through the angels defenses by expertly dodging its tentacles. As he noticed that he only had fifteen seconds internal battery power left Shinji rolled under the angel's tentacles he landed right in from of the angels core. He yelled using a jutsu," Chidori." focusing its energy around his kunai. When he struck the angels core with the kunai it went straight through and out the back of the angel's body. Five seconds later the Eva shut down and Shinji not worrying sat back in his seat and closed his eyes and falling asleep. Half an hour later the recovery team got to the Eva and got Shinji out of the entry plug. The moment Shinji stepped onto the ground Section 2 agents swarmed him and put handcuffs on him leading him back to Nerv HQ via access elevators. On the way to the holding cell Shinji was going to spend the night in he walked past Ritsuko and decided it was now or never to ask her something. "Uh... Ritsuko i know this isn't my place right now but could you see if you can add those tentacles from the angel onto mine and Rei's Eva's. It would be a shame to see such good weapons go to waste." He asked her innocently.

"Sure Shinji" She told him thinking' were did he get such knowledge of battle and strategies.

That night when he got back to the apartment with Misato he decided to ask her something important." Hey Misato can i take Rei, Toji and Kenske on a trip for survival training to become Shinobi." he asked hr sweetly.

After a few minutes of thinking she decided that it be ok." Sure Shinji but how are you going to get Rei ad yourself back to HQ if an angel attacks."

"Misato have you forgotten that i can teleport myself and Rei back here." He said rolling his eyes and scaring her by appearing behind her.

"uuuu..." was all she could manage to say.

"Thanks Misato. We'll be gone for about six months so could you figure something out for school and don't tell Gendo." he said

"Sure Shinji."Misato replied thinking of an excuse for the kids why they won't be attending school.

A week later. Training camp

It was Shinji's first day of teaching them on how to become Shinobi's. He first taught them the basics of chakra and what it's made up of. "This first training exercise was to climb a tree" he told them.

"but the catch is you can't use your hands." he explained further.

"How are we supposed to do that?" Toji asked complaining.

"Here let me demonstrate" he told the three.

Rei thought that he would make it up the tree without using his hands like he told them. Toji thought he was going to step on the tree ad lands on his ass and Kenske didn't know what to think. Shinji walked up to the nearest tree and put on foot firmly against it and lifted his other foot off the ground and walked to the top of the tree and back down twice to prove his point. Shinji then explained that you need to concentrate your chakra to change your center of gravity and stand against the tree. He also explained that it was an exercise for them to learn chakra control. He then took out tree kunai's and threw them at their feet.

"Use them to mark the highest point you can get on the tree. You will need to run at the tree and use your momentum for now." He added.

Rei was the first to react and picked up her kunai and walked so she was in front of a tree. Toji started running at the tree first and made it two feet up before he fall backwards, Kenske made it further than Toji but was blown of the tree and he made a large dent from where he jumped off .

"Not bad for your first try guys. Toji you didn't use enough of your chakra that's why you fell down, try and concentrate a little more. Kenske you used to much. That's why you were thrown off the tree." He said pointing the dent he made in the tree." And it looks like Rei has mastered the technique already. Okay Toji and Kenske; keep trying to get further than your last mark. Meanwhile I'm going to start training you Rei with a more advanced technique." He said adding the last part while looking at Rei and started walking towards the lake. Rei followed him thinking about what he was going to teach her now.

"You're doing really well Rei" he told her" I didn't really expect you to get it right on your first try, but otherwise you doing really great."

"Thank you Shinji" She said moving her hand to hold his.

Shinji noticed this and blushed at the thought. He then thought to himself,' why I am blushing. Its these damn hormones.' Shinji moved his hands closer to Rei's and she saw that and moved her hand the rest of the way. She blushed slightly when their hands touched Rei blushed slightly but Shinji move his hand completely into hers and held it firmly.

"Rei, focus a little more chakra in your feet than when you did with the tree and don't panic ok?" he said asking her.

"Yes Shinji." She said and he could feel some of her chakra amass in her feet. By now they had reached the water's edge but Shinji was still going to take a step onto the water.

"Now keep walking Rei." He said to her encouragingly

She was a little confused but realized what he meant when she saw one of his feet were resting on the water. She looked at him and he flashed her his foxy grin. Understanding what was going to happen she confidently took a step onto the water but her foot went slightly underneath the water so Shinji told her," concentrate a little more chakra Rei." When she did what Shinji told her, her foot rose above the water and floated on top of it. She lifted her other foot of the ground and put it on the water. When she looked up at Shinji she saw he had a huge grin plastered across his face.

"I knew you could do it Rei. Hold on one sec." He said making a hand sign and in a puff of smoke a clone of Shinji and it started running to where Toji and Kenske were.

"Rei, even though we haven't known each other that long I know this and I want you to know it as well." He took a deep breath and started again." Rei, I love you." He finished looking into her eyes.

"I – I love you too Shinji." She replied closing her eyes and leaning toward him. Shinji got the message and they shared their first kiss together.

**A/N: aw how sweet. Reviews are welcome just no destructive critisisism please. Also look at my other story and I want to start a new crossover. It'll be a surprise so you'll have to wait.**


	6. Chapter 6

Chapter 6: Angel #5 and survival training

The next day came way too early for Kenske and Toji. They were still tired and sore from falling of their trees during yesterdays training. Shinji had so far taught all three of them survival training, catching fish and collecting berries. They had separate tents and had trained very hard.

Shinji and Rei were up earlier than the other two and were talking while they were catching fish for breakfast. He had already explained to Rei that they were going to be alone for their experience in survival training. Other than that they talked to each other a lot, they had learnt a lot about each other. Shinji was unimpressed by what Gendo did to Rei to make her have such a boring life before he came. They were slowly changing that, Rei now went outside more. Mostly on dates with Shinji but sometimes buy herself to get food and new clothes. Rei had her own opinions and started doing what she wanted and not only what other people wanted her to do. She had emotion in her voice instead of the monotone voice she had.

Shinji and Rei had caught enough fish for breakfast and decided to lie down before going back to their camp. Rei and Shinji sat close to each other and Shinji had his arm around Rei's waist holding her tightly."Rei, have you ever thought what you want to do after all the angels are gone?"He asked her his voice just above a whisper.

Rei then felt guilty. She knew that after all the angels are that she would cause Third Impact and kill everyone."I haven't really thought about that Shinji what about you."Rei replied.

"I want to settle down and raise a family with this beautiful blue headed girl I met. She is very nice, has a beautiful smile and I know that she loves me as well." He told her giving her a kiss on her forehead.

Rei blushed and smiled slightly when he finished."We should get back before Toji and Kenske wonder where we are." He said standing up and holding his hand out for her."We need to tell them about us Rei. But I think it would be better to tell them sooner than later."

"Yes but I think we should rather wait until the end of our survival training."Rei said giving him an ultimatum.

"Yea your right Rei." Shinji replied with a small sigh.

Back in the campsite Toji and Kenske were getting dressed and got outside their tents waiting for Shinji-sensei and Rei. When five minutes passed they got curious and started walking towards the lake to see if they were there. What they saw shocked them both. They saw Shinji kissing Rei and his arm around her waist. They both quietly tiptoed back toward the campsite and sat around the fire that Shinji probably made before he went off with Rei."I don't think we should tell them what we saw, if Shinji-sensei thought that we should know about him and Rei he would've told us and I'm sure that he is goi…." Just then the angel alarms went off in Tokyo 3. Toji and Kenske ran to the underground shelter that Shinji had made in case of an attack while Shinji transported both himself and Rei to Nerv.

"What's the targets status?" Misato asked no one in particular. The angel she was looking at had a double pyramid form.

"The angel is moving at 2.5 kilometers at the moment and has made no attacks of any sort."Maya yelled back.

"Where are Shinji and Rei?" Misato asked. She was startled when a voice answered her that was next to her.

"I'm right here Misato no need to yell." Shinji answered her rubbing his ears.

When she looked at him she saw that he was already suited up and ready to go."Ok, Shinji get into your and await further orders."

"Yes Misato." He said giving her a mock salute. He then disappeared in a puff of white smoke and reappeared in his Eva's entry plug. While he sat there getting ready he was being briefed on where his Eva's new weapons were."You remember where your Shurikens and Kunai's are and the new angel weaponry is in a slot underneath each of the Eva's wrists" Ritsuko explained to him.

"Eva Launch!." Misato yelled.

As the Eva raced to the surface there was a problem."Ma'am we're detecting a high energy build up I the target."Maya told Misato worryingly.

"Shit, not now!"Misato said.

When Shinji heard Misato say that he saw the angel was shining brightly along its edges."Shit."Shinji said.

When the angel fired its beam Misato yelled."SSSShiiiiinji."

"jeez no need to yell Misato."A voice said behind her.

When she turned around she was shocked, surprised and relieved that Shinji was here. She ran up to him and grabbed him into a hug.' but wait if he's here then what's in his entry plug' when she looked she saw it was a log of wood.

"Substitution jutsu." He told her answering the question she hadn't asked yet.


	7. Chapter 7

**A/N: I wanna thank all my followers,**

Sangai-Havoc

UltraRiderSenshiChronix

duskrider

guardsmansparky

jacketslacker

**And the reviewers. If you guys have any suggestions that may make my story a bit better. Feel free to tell me about them.**

On with the story

Shinji, Misato and Ritsuko were in a briefing room of sorts going over the data they got from the angel and were trying to figure out how to destroy it. The angel was currently drilling a hole towards the GeoFront and would break through all twenty two layers of steel in sixteen hours.

"Offense and defense its nearly perfect. A real flying fortress." Misato thought out loud.

After a few moments of silence Shinji saw a way to kill the angel."There." he said and Misato looked confused.

"Where?" she asked stupidly

Putting his hands on the map lifting them turning the map 3D." we can shoot the angel with a laser or something powerful from the top of this mountain." He said" but we'd need all the power of Japan to do that. We can also channel half of Tokyo 3's power into my Eva and I can charge up a mass energy conversion. I can keep it stable in my A.T. Field and throw it at the angel. For both of these plans I'd need unit 00 covering my Eva with a shield in case the angel shoots again." He pointed to specific locations on the map while he talked." So what do the Magi say, which plan will be more likely to succeed?" he finished looking at Ritsuko.

Misato and Ritsuko were dumbstruck at how Shinji could come up with those plans in less than five minutes and co-ordinate them strategically.' Wisdom beyond his years' Misato thought to herself.

"uuuuh." She mumbled still dumbstruck looking at her phone." The Magi give your first plan a 45.3% chance and your second plan a 67.9% chance of succeeding. So Shinji it looks like you have to practice your mass energy conversion." She said starting to walk towards the door.

**Later that day.**

Shinji had practiced the energy conversion to near perfection. He could only do an imperfect conversion otherwise the buildup of energy would decimate all of Japan; Ritsuko had told him before he started practicing. She had thought of what they could use as a shield and after an hour of thinking she decided to use the top of Nerv's Space shuttle." It looks big and clunky." Misato told her.

"It may not be one for looks but it has poly urethane coating so it will stand up against the Angel's particle beam for 17 seconds."Ritsuko explained.

"Eva Launch." Misato said as the Eva's came out of the side of a mountain. Shinji opened a personal com to Rei to talk to her.

"Hey Rei, how you feel?" he asked her concerned.

"I am fine Shinji, is there anything else you want to ask?"Rei asked him.

"Not really Rei, but if the Angel shoots at us don't use the shield ok. Use your jutsu. Promise that."Shinji replied.

"Sure Shinji promise. "She said changing back to her monotone voice and opening the com with HQ again."Approaching the target zone Major."

"Very good Rei." Misato replied

Two hours later

"Alright, Shinji and Rei." a voice said behind them."It's time to go."

"Alright Misato. But you don't need to sound so grim when you tell us this." Shinji said sarcastically

"Sorry Shinji. I'm just really on edge right now." Misato explained to him.

" Relax Misato. We're going to kill this Angel and then we can get back into our normal routine. Well as normal as our life can get." Shinji said with a small chuckle.

" Yea. Ok, you get in your Eva's and lets do this." Misato ordered the enthusiastically.

In the Eva

" Ok Shinji. We are trusting you with half of Tokyo 3's power. You have to kill this angel with your first shot. Rei, if the angel attacks we need you to protect Shinji." She told the two.

" Yes ma'am" Shinji said giving her a mock salute then walking his Eva to the attack spot.

Shinji started charging up the ball of energy that was being held back by only his A.T. Shinji had almost reached the peak of the energy conversion the angel decided to attack.

"Ma'am. We are detecting a large energy amassing inside the angel." one of the bridge bunnies reported to her.

Before Misato could say anything Rei flashed back to her training with Shinji and his other two students. They had discovered their element jutsu's and had begun training in them. Lucky for Rei, Shinji had the same bloodline limit as her.

"Ok, Rei. Now focus on forming a barrier in front of you. Control both elements and merge them so they are one." he said to her.

Rei threw her Eva's shiled away and performed the jutsu."Reflecting mirror: Ice jutsu." she said and a mass of water shot from the ground in front of Shinji's Eva and crystalised protecting him from the Angel's particle beam.

Just as the Angel's beam hit the shield Shinji threw the energy ball which cut through its beam. As the ball raced towards the angel Rei dropped the shield and her Eva fell to the ground. Without a second thought Shinji dropped his Eva down and manually ejected her entry plug. Jumping down to the ground Shinji ran to her plug and opened the door.

"Rei, Rei. Are you okay?" he asked frantically.

"Yes, Shinji. I'm over here" she replied calmly getting out of the entry plug.

"Here, let me help you." he told her picking her up bridal style and she leaned her head against his chest and started to sob."What's wrong Rei." He asked her worried.

"I nearly lost you Sh- Shinji." she sobbed as Shinji laid her down under a nearby tree.

"Its ok Rei. You are never going to lose me, I promise." he said giving her a passionate kiss on the lips.

"Aaw, that's so sweet" Misato said as she looked at the two of them.

'Maybe I should report this to the Commander'. Ritsuko thought before she saw a camera fixed on the tw of them.' I guess he already knows.'


End file.
